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Bioinstrumentation scholars: you are welcome to edit and improve this course wiki. Correct, helpful, exquisitely-expressed changes will increase your class participation grade. Alterations not meeting those critera may have the opposite effect.

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Contents 1 20.309 course information 2 20.345 course information 3 Optical microscopy lab wiki pages 3.1 Lab manuals 3.2 Code examples and simulations 3.3 Background reading 4 Electronics mini-lab 4.1 Background reading 5 DNA melting lab 5.1 Lab manuals 5.2 Code examples and simulations 5.3 Reference materials 5.4 Background reading 6 Limits of detection lab 7 MRI mini-lab 8 Useful things 8.1 Resource lists 8.2 Matlab tutorials 9 Projects

20.309 course information

• 20.309:Course Information
• 20.309:Lab Report Guidelines
• 20.309:Safety

Reserve a lab station here: Bioinstrumentation Lab reservation system

20.345 course information

• 20.345:Course_Information

Optical microscopy lab wiki pages

Lab manuals

• Lab Manual: Optical Microscopy
• Optical Microscopy Part 1: Brightfield Microscopy
• Optical Microscopy Part 2: Fluorescence Microscopy
• Optical Microscopy Part 3: Resolution and Stability
• Optical Microscopy Part 4: Particle Tracking
• Optical Microscopy Report Outline

Code examples and simulations

• Converting Gaussian fit to Rayleigh resolution
• MATLAB: Estimating resolution from a PSF slide image

Background reading

• Geometrical optics and ray tracing
• Physical optics and resolution
• Optical detectors, noise, and the limit of detection
• Cellular microrheology
• Protocols for cell culture

Electronics mini-lab

• Electronics Mini-Lab

Background reading

• Electronics primer
• Real electronics

DNA melting lab

Lab manuals

• Lab Manual:Measuring DNA Melting Curves
• DNA Melting Part 1: Measuring Temperature and Fluorescence
• DNA Melting Report Requirements for Part 1
• DNA Melting Part 2: Lock-in Amplifier and Temperature Control
• DNA Melting: Model function and parameter estimation by nonlinear regression
• DNA Melting Report Requirements for Part 2

Code examples and simulations

• DNA Melting: Simulating DNA Melting - Basics
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• DNA Melting: Model function and parameter estimation by nonlinear regression

Reference materials

• DNA Melting Thermodynamics
• DNA Melting: DNA Sequences
• DINAMelt Web Server

Background reading

• Electronics Primer

Limits of detection lab

• Limits of Detection:Report Requirements
• Lab Manual: Limits of Detection
• Limits of Detection: Data Sessions

MRI mini-lab

• MGH tabletop MRI

(Kept for historical reasons.)

Useful things

Resource lists

• Technical Writing
• Resource list: Optics
• Resource list: Optical trapping
• Resource list: Magnetic Resonance Imaging
• Resource list: DNA melting and PCR
• Resource list: Particle tracking
• Resource list: Microscopy
• Resource list: Matlab
• Resource list: Image Enhancement
• Resource list: Suppliers
• Resource list: Electronics
• Resource list: Image processing

Matlab tutorials

• Resource list: Image Enhancement
• Resource list: Matlab
• DNA Melting: Simulating DNA Melting - Basics
• Matlab:Image Processing for Fluorescent Microscopy
• Matlab:Division operators
• Matlab:DNA Melting Data Analysis
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• Matlab:Matlab Fundamentals

Projects

• eSTORM: super-resolution microscope for the classroom